null Mon 24 Dec 08:01:40 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2f4p-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2f4p-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2f4p-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2f4p-3.8-parrot-noncs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2f4p-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2f4p-3.8-parrot-noncs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Mon 24 Dec 08:01:44 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2f4p-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2f4p-3.8-parrot-noncs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 373 and 0 Target number of residues in the AU: 373 Target solvent content: 0.6398 Checking the provided sequence file Detected sequence length: 147 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 588 Adjusted target solvent content: 0.43 Input MTZ file: 2f4p-3.8-parrot-noncs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 170 Cell parameters: 71.746 71.746 188.600 90.000 90.000 120.000 Input sequence file: 2f4p-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 4704 target number of atoms Had to go as low as 0.65 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 21.543 3.800 Wilson plot Bfac: 71.67 5384 reflections ( 99.39 % complete ) and 0 restraints for refining 5234 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.3478 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3295 (Rfree = 0.000) for 5234 atoms. Found 28 (28 requested) and removed 89 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.55 3.90 Search for helices and strands: 0 residues in 0 chains, 5226 seeds are put forward NCS extension: 0 residues added, 5226 seeds are put forward Round 1: 153 peptides, 34 chains. Longest chain 9 peptides. Score 0.229 Round 2: 228 peptides, 45 chains. Longest chain 11 peptides. Score 0.323 Round 3: 233 peptides, 41 chains. Longest chain 12 peptides. Score 0.389 Round 4: 231 peptides, 39 chains. Longest chain 13 peptides. Score 0.408 Round 5: 260 peptides, 44 chains. Longest chain 15 peptides. Score 0.428 Taking the results from Round 5 Chains 44, Residues 216, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5384 reflections ( 99.39 % complete ) and 10112 restraints for refining 4253 atoms. 9292 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2917 (Rfree = 0.000) for 4253 atoms. Found 19 (23 requested) and removed 70 (11 requested) atoms. Cycle 2: After refmac, R = 0.2803 (Rfree = 0.000) for 4128 atoms. Found 23 (23 requested) and removed 50 (11 requested) atoms. Cycle 3: After refmac, R = 0.2803 (Rfree = 0.000) for 4042 atoms. Found 22 (22 requested) and removed 41 (11 requested) atoms. Cycle 4: After refmac, R = 0.2777 (Rfree = 0.000) for 3976 atoms. Found 22 (22 requested) and removed 68 (11 requested) atoms. Cycle 5: After refmac, R = 0.2553 (Rfree = 0.000) for 3906 atoms. Found 21 (21 requested) and removed 43 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.63 3.99 Search for helices and strands: 0 residues in 0 chains, 4007 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 4026 seeds are put forward Round 1: 210 peptides, 46 chains. Longest chain 10 peptides. Score 0.254 Round 2: 244 peptides, 43 chains. Longest chain 13 peptides. Score 0.396 Round 3: 245 peptides, 45 chains. Longest chain 11 peptides. Score 0.374 Round 4: 267 peptides, 46 chains. Longest chain 14 peptides. Score 0.424 Round 5: 267 peptides, 42 chains. Longest chain 15 peptides. Score 0.470 Taking the results from Round 5 Chains 44, Residues 225, Estimated correctness of the model 0.0 % 4 chains (27 residues) have been docked in sequence ------------------------------------------------------ 5384 reflections ( 99.39 % complete ) and 8784 restraints for refining 3961 atoms. 7819 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2781 (Rfree = 0.000) for 3961 atoms. Found 21 (21 requested) and removed 65 (10 requested) atoms. Cycle 7: After refmac, R = 0.2660 (Rfree = 0.000) for 3863 atoms. Found 21 (21 requested) and removed 71 (10 requested) atoms. Cycle 8: After refmac, R = 0.2519 (Rfree = 0.000) for 3773 atoms. Found 20 (20 requested) and removed 34 (10 requested) atoms. Cycle 9: After refmac, R = 0.2732 (Rfree = 0.000) for 3724 atoms. Found 20 (20 requested) and removed 48 (10 requested) atoms. Cycle 10: After refmac, R = 0.2702 (Rfree = 0.000) for 3674 atoms. Found 20 (20 requested) and removed 45 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.56 3.91 Search for helices and strands: 0 residues in 0 chains, 3789 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 3805 seeds are put forward Round 1: 230 peptides, 48 chains. Longest chain 10 peptides. Score 0.291 Round 2: 260 peptides, 47 chains. Longest chain 13 peptides. Score 0.393 Round 3: 273 peptides, 45 chains. Longest chain 12 peptides. Score 0.452 Round 4: 276 peptides, 49 chains. Longest chain 11 peptides. Score 0.413 Round 5: 287 peptides, 47 chains. Longest chain 16 peptides. Score 0.466 Taking the results from Round 5 Chains 47, Residues 240, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 5384 reflections ( 99.39 % complete ) and 8872 restraints for refining 3947 atoms. 7911 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2826 (Rfree = 0.000) for 3947 atoms. Found 21 (21 requested) and removed 74 (10 requested) atoms. Cycle 12: After refmac, R = 0.2481 (Rfree = 0.000) for 3844 atoms. Found 21 (21 requested) and removed 42 (10 requested) atoms. Cycle 13: After refmac, R = 0.2515 (Rfree = 0.000) for 3793 atoms. Found 21 (21 requested) and removed 33 (10 requested) atoms. Cycle 14: After refmac, R = 0.2532 (Rfree = 0.000) for 3754 atoms. Found 20 (20 requested) and removed 30 (10 requested) atoms. Cycle 15: After refmac, R = 0.2448 (Rfree = 0.000) for 3719 atoms. Found 18 (20 requested) and removed 27 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.56 3.91 Search for helices and strands: 0 residues in 0 chains, 3803 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3821 seeds are put forward Round 1: 192 peptides, 38 chains. Longest chain 13 peptides. Score 0.303 Round 2: 235 peptides, 40 chains. Longest chain 15 peptides. Score 0.407 Round 3: 252 peptides, 43 chains. Longest chain 21 peptides. Score 0.418 Round 4: 257 peptides, 43 chains. Longest chain 14 peptides. Score 0.432 Round 5: 260 peptides, 44 chains. Longest chain 11 peptides. Score 0.428 Taking the results from Round 4 Chains 43, Residues 214, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5384 reflections ( 99.39 % complete ) and 8447 restraints for refining 3773 atoms. 7634 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3019 (Rfree = 0.000) for 3773 atoms. Found 20 (20 requested) and removed 80 (10 requested) atoms. Cycle 17: After refmac, R = 0.2546 (Rfree = 0.000) for 3679 atoms. Found 20 (20 requested) and removed 35 (10 requested) atoms. Cycle 18: After refmac, R = 0.2567 (Rfree = 0.000) for 3638 atoms. Found 20 (20 requested) and removed 38 (10 requested) atoms. Cycle 19: After refmac, R = 0.2443 (Rfree = 0.000) for 3595 atoms. Found 19 (19 requested) and removed 20 (9 requested) atoms. Cycle 20: After refmac, R = 0.2273 (Rfree = 0.000) for 3575 atoms. Found 19 (19 requested) and removed 19 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.51 3.86 Search for helices and strands: 0 residues in 0 chains, 3694 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 3712 seeds are put forward Round 1: 185 peptides, 40 chains. Longest chain 7 peptides. Score 0.253 Round 2: 251 peptides, 45 chains. Longest chain 12 peptides. Score 0.391 Round 3: 259 peptides, 47 chains. Longest chain 10 peptides. Score 0.390 Round 4: 257 peptides, 41 chains. Longest chain 14 peptides. Score 0.455 Round 5: 264 peptides, 41 chains. Longest chain 20 peptides. Score 0.474 Taking the results from Round 5 Chains 42, Residues 223, Estimated correctness of the model 0.0 % 2 chains (27 residues) have been docked in sequence ------------------------------------------------------ 5384 reflections ( 99.39 % complete ) and 8262 restraints for refining 3807 atoms. 7305 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2467 (Rfree = 0.000) for 3807 atoms. Found 20 (20 requested) and removed 48 (10 requested) atoms. Cycle 22: After refmac, R = 0.2350 (Rfree = 0.000) for 3754 atoms. Found 20 (20 requested) and removed 36 (10 requested) atoms. Cycle 23: After refmac, R = 0.2734 (Rfree = 0.000) for 3711 atoms. Found 20 (20 requested) and removed 62 (10 requested) atoms. Cycle 24: After refmac, R = 0.2514 (Rfree = 0.000) for 3638 atoms. Found 20 (20 requested) and removed 48 (10 requested) atoms. Cycle 25: After refmac, R = 0.2284 (Rfree = 0.000) for 3595 atoms. Found 19 (19 requested) and removed 24 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.49 3.83 Search for helices and strands: 0 residues in 0 chains, 3684 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 3700 seeds are put forward Round 1: 218 peptides, 45 chains. Longest chain 8 peptides. Score 0.292 Round 2: 255 peptides, 46 chains. Longest chain 13 peptides. Score 0.390 Round 3: 241 peptides, 39 chains. Longest chain 11 peptides. Score 0.436 Round 4: 230 peptides, 36 chains. Longest chain 11 peptides. Score 0.441 Round 5: 246 peptides, 38 chains. Longest chain 18 peptides. Score 0.461 Taking the results from Round 5 Chains 39, Residues 208, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 5384 reflections ( 99.39 % complete ) and 8637 restraints for refining 3896 atoms. 7794 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2533 (Rfree = 0.000) for 3896 atoms. Found 21 (21 requested) and removed 76 (10 requested) atoms. Cycle 27: After refmac, R = 0.2465 (Rfree = 0.000) for 3811 atoms. Found 21 (21 requested) and removed 40 (10 requested) atoms. Cycle 28: After refmac, R = 0.2403 (Rfree = 0.000) for 3775 atoms. Found 20 (20 requested) and removed 33 (10 requested) atoms. Cycle 29: After refmac, R = 0.2315 (Rfree = 0.000) for 3745 atoms. Found 20 (20 requested) and removed 30 (10 requested) atoms. Cycle 30: After refmac, R = 0.2713 (Rfree = 0.000) for 3725 atoms. Found 20 (20 requested) and removed 45 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.69 4.05 Search for helices and strands: 0 residues in 0 chains, 3800 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 3815 seeds are put forward Round 1: 177 peptides, 37 chains. Longest chain 9 peptides. Score 0.268 Round 2: 194 peptides, 36 chains. Longest chain 9 peptides. Score 0.336 Round 3: 207 peptides, 38 chains. Longest chain 11 peptides. Score 0.350 Round 4: 189 peptides, 32 chains. Longest chain 11 peptides. Score 0.374 Round 5: 198 peptides, 33 chains. Longest chain 12 peptides. Score 0.388 Taking the results from Round 5 Chains 33, Residues 165, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5384 reflections ( 99.39 % complete ) and 8703 restraints for refining 3842 atoms. 8076 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2740 (Rfree = 0.000) for 3842 atoms. Found 21 (21 requested) and removed 70 (10 requested) atoms. Cycle 32: After refmac, R = 0.2602 (Rfree = 0.000) for 3774 atoms. Found 20 (20 requested) and removed 65 (10 requested) atoms. Cycle 33: After refmac, R = 0.2513 (Rfree = 0.000) for 3707 atoms. Found 20 (20 requested) and removed 30 (10 requested) atoms. Cycle 34: After refmac, R = 0.2346 (Rfree = 0.000) for 3676 atoms. Found 20 (20 requested) and removed 25 (10 requested) atoms. Cycle 35: After refmac, R = 0.2516 (Rfree = 0.000) for 3652 atoms. Found 20 (20 requested) and removed 34 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.53 3.88 Search for helices and strands: 0 residues in 0 chains, 3748 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 3762 seeds are put forward Round 1: 149 peptides, 31 chains. Longest chain 10 peptides. Score 0.258 Round 2: 178 peptides, 32 chains. Longest chain 12 peptides. Score 0.340 Round 3: 180 peptides, 29 chains. Longest chain 11 peptides. Score 0.387 Round 4: 188 peptides, 30 chains. Longest chain 17 peptides. Score 0.397 Round 5: 187 peptides, 27 chains. Longest chain 16 peptides. Score 0.433 Taking the results from Round 5 Chains 27, Residues 160, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 5384 reflections ( 99.39 % complete ) and 8066 restraints for refining 3647 atoms. 7424 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2673 (Rfree = 0.000) for 3647 atoms. Found 20 (20 requested) and removed 35 (10 requested) atoms. Cycle 37: After refmac, R = 0.2514 (Rfree = 0.000) for 3604 atoms. Found 19 (19 requested) and removed 27 (9 requested) atoms. Cycle 38: After refmac, R = 0.2442 (Rfree = 0.000) for 3576 atoms. Found 19 (19 requested) and removed 22 (9 requested) atoms. Cycle 39: After refmac, R = 0.2862 (Rfree = 0.000) for 3558 atoms. Found 19 (19 requested) and removed 31 (9 requested) atoms. Cycle 40: After refmac, R = 0.2671 (Rfree = 0.000) for 3526 atoms. Found 19 (19 requested) and removed 34 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.58 3.93 Search for helices and strands: 0 residues in 0 chains, 3633 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3651 seeds are put forward Round 1: 115 peptides, 25 chains. Longest chain 7 peptides. Score 0.227 Round 2: 150 peptides, 28 chains. Longest chain 14 peptides. Score 0.305 Round 3: 136 peptides, 26 chains. Longest chain 12 peptides. Score 0.287 Round 4: 128 peptides, 21 chains. Longest chain 17 peptides. Score 0.335 Round 5: 158 peptides, 26 chains. Longest chain 12 peptides. Score 0.360 Taking the results from Round 5 Chains 26, Residues 132, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 5384 reflections ( 99.39 % complete ) and 7461 restraints for refining 3403 atoms. 6927 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2733 (Rfree = 0.000) for 3403 atoms. Found 18 (18 requested) and removed 43 (9 requested) atoms. Cycle 42: After refmac, R = 0.2585 (Rfree = 0.000) for 3360 atoms. Found 18 (18 requested) and removed 37 (9 requested) atoms. Cycle 43: After refmac, R = 0.2271 (Rfree = 0.000) for 3329 atoms. Found 18 (18 requested) and removed 15 (9 requested) atoms. Cycle 44: After refmac, R = 0.2389 (Rfree = 0.000) for 3326 atoms. Found 18 (18 requested) and removed 26 (9 requested) atoms. Cycle 45: After refmac, R = 0.2404 (Rfree = 0.000) for 3306 atoms. Found 18 (18 requested) and removed 19 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.54 3.89 Search for helices and strands: 0 residues in 0 chains, 3392 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 3407 seeds are put forward Round 1: 165 peptides, 34 chains. Longest chain 10 peptides. Score 0.270 Round 2: 194 peptides, 36 chains. Longest chain 11 peptides. Score 0.336 Round 3: 203 peptides, 34 chains. Longest chain 17 peptides. Score 0.389 Round 4: 195 peptides, 32 chains. Longest chain 12 peptides. Score 0.392 Round 5: 194 peptides, 33 chains. Longest chain 12 peptides. Score 0.376 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 32, Residues 163, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2f4p-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5384 reflections ( 99.39 % complete ) and 7524 restraints for refining 3439 atoms. 6904 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2333 (Rfree = 0.000) for 3439 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.2414 (Rfree = 0.000) for 3410 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.2374 (Rfree = 0.000) for 3389 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.2321 (Rfree = 0.000) for 3375 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:46:10 GMT 2018 Job finished. TimeTaking 44.52 Used memory is bytes: 3388480